`Unexpected Node Type (9) found, expecting LongKeyNode` in diff tool

[axd1x8a]

Describe the bug
When I use the diff tool, an exception is thrown:

2026-02-17 22:11:50 ERROR (CreateDiffTask) Task Error: Checking Program Differences - Uncaught Exception: ghidra.util.exception.AssertException: Unexpected Node Type (9) 
found, expecting LongKeyNode ghidra.util.exception.AssertException: Unexpected Node Type (9) found, expecting LongKeyNode
	at db.NodeMgr.getLongKeyNode(NodeMgr.java:273)
	at db.LongKeyInteriorNode.getLeafNode(LongKeyInteriorNode.java:414)
	at db.LongKeyInteriorNode.getLeafNode(LongKeyInteriorNode.java:416)
	at db.LongKeyInteriorNode.getLeafNode(LongKeyInteriorNode.java:416)
	at db.Table.getRecord(Table.java:701)
	at ghidra.program.database.references.ToAdapterV1.getRefList(ToAdapterV1.java:76)
	at ghidra.program.database.references.ReferenceDBManager.getToRefs(ReferenceDBManager.java:1642)
	at ghidra.program.database.references.ReferenceDBManager.isExternalEntryPoint(ReferenceDBManager.java:1560)
	at ghidra.program.database.symbol.SymbolManager.isExternalEntryPoint(SymbolManager.java:1454)
	at ghidra.program.database.symbol.MemorySymbol.isExternalEntryPoint(MemorySymbol.java:73)
	at ghidra.program.util.ProgramDiff$SymbolComparator.isSame(ProgramDiff.java:2090)
	at ghidra.program.util.ProgramDiff$SymbolComparator.isSame(ProgramDiff.java:2079)
	at ghidra.program.util.ProgramDiff$ProgramDiffComparatorImpl.getObjectDiffs(ProgramDiff.java:1986)
	at ghidra.program.util.ProgramDiff.getLabelDifferences(ProgramDiff.java:1440)
	at ghidra.program.util.ProgramDiff.createAddressSet(ProgramDiff.java:974)
	at ghidra.program.util.ProgramDiff.getDifferences(ProgramDiff.java:512)
	at ghidra.program.util.ProgramMergeManager.getFilteredDifferences(ProgramMergeManager.java:147)
	at ghidra.app.plugin.core.diff.DiffController.getFilteredDifferences(DiffController.java:160)
	at ghidra.app.plugin.core.diff.CreateDiffTask.run(CreateDiffTask.java:80)
	at ghidra.util.task.Task.monitoredRun(Task.java:134)
	at ghidra.util.task.TaskRunner.lambda$startTaskThread$0(TaskRunner.java:106)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1095)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:619)
	at java.base/java.lang.Thread.run(Thread.java:1447)

When I select the functions option only, I can see the differences, but I can't apply all of them:

2026-02-17 22:34:42 ERROR (ApplyDiffCommand) Error Applying Diff: An error occurred while applying differences.
Only some of the differences may have been applied. ghidra.util.exception.AssertException: Unexpected Node Type (9) found, expecting LongKeyNode
	at db.NodeMgr.getLongKeyNode(NodeMgr.java:273)
	at db.LongKeyInteriorNode.getLeafNode(LongKeyInteriorNode.java:414)
	at db.LongKeyInteriorNode.getLeafNode(LongKeyInteriorNode.java:416)
	at db.LongKeyInteriorNode.getLeafNode(LongKeyInteriorNode.java:416)
	at db.Table.getRecord(Table.java:701)
	at ghidra.program.database.references.ToAdapterV1.getRefList(ToAdapterV1.java:76)
	at ghidra.program.database.references.ReferenceDBManager.getToRefs(ReferenceDBManager.java:1642)
	at ghidra.program.database.references.ReferenceDBManager.isExternalEntryPoint(ReferenceDBManager.java:1560)
	at ghidra.program.database.symbol.SymbolManager.isExternalEntryPoint(SymbolManager.java:1454)
	at ghidra.program.database.symbol.MemorySymbol.isExternalEntryPoint(MemorySymbol.java:73)
	at ghidra.program.util.ProgramDiff$SymbolComparator.isSame(ProgramDiff.java:2090)
	at ghidra.program.util.ProgramDiff$SymbolComparator.isSame(ProgramDiff.java:2079)
	at ghidra.program.util.ProgramDiff$ProgramDiffComparatorImpl.getObjectDiffs(ProgramDiff.java:1986)
	at ghidra.program.util.ProgramDiff.getLabelDifferences(ProgramDiff.java:1440)
	at ghidra.program.util.ProgramDiff.createAddressSet(ProgramDiff.java:974)
	at ghidra.program.util.ProgramDiff.getDifferences(ProgramDiff.java:512)
	at ghidra.program.util.ProgramMergeManager.mergeLabels(ProgramMergeManager.java:827)
	at ghidra.program.util.ProgramMergeManager.merge(ProgramMergeManager.java:452)
	at ghidra.program.util.ProgramMergeManager.merge(ProgramMergeManager.java:404)
	at ghidra.app.plugin.core.diff.DiffController.apply(DiffController.java:207)
	at ghidra.app.plugin.core.diff.ApplyDiffCommand.analysisWorkerCallback(ApplyDiffCommand.java:60)
	at ghidra.app.plugin.core.analysis.AutoAnalysisManager$AnalysisWorkerCommand.applyTo(AutoAnalysisManager.java:1699)
	at ghidra.app.plugin.core.analysis.AutoAnalysisManager$AnalysisWorkerCommand.applyToWithTransaction(AutoAnalysisManager.java:1647)
	at ghidra.app.plugin.core.analysis.AutoAnalysisManager.scheduleWorker(AutoAnalysisManager.java:1355)
	at ghidra.app.plugin.core.diff.ApplyDiffCommand.applyTo(ApplyDiffCommand.java:83)
	at ghidra.app.plugin.core.diff.ApplyDiffCommand.applyTo(ApplyDiffCommand.java:39)
	at ghidra.framework.plugintool.mgr.BackgroundCommandTask.run(BackgroundCommandTask.java:103)
	at ghidra.framework.plugintool.mgr.ToolTaskManager.run(ToolTaskManager.java:347)
	at java.base/java.lang.Thread.run(Thread.java:1447)

I also saw these errors, but I'm not sure if they are related:

2026-02-17 22:27:42 ERROR (ProgramDataTypeManager) java.lang.IllegalAccessException: class ghidra.program.database.data.DataTypeManagerDB cannot access a member of class ghidra.program.model.data.BadDataType with modifiers "private"  
2026-02-17 22:27:42 ERROR (ProgramDataTypeManager) java.lang.IllegalAccessException: class ghidra.program.database.data.DataTypeManagerDB cannot access a member of class ghidra.program.model.data.BadDataType with modifiers "private" 

To Reproduce
Steps to reproduce the behavior:

1. Copy the program and make some changes to the copy
2. Use diff tool to diff it with original program
3. See error

Environment (please complete the following information):

• OS: windows
• Java Version: 21
• Ghidra Version: 12.0.3
• Ghidra Origin: github releases

[ghidra1]

It sounds like the database for that program has become corrupt. It is impossible to say how it got into that state. With close examination of the database I can like identify what is bad, but there will likely be no way to reason how it got into that state. I have seen cases where it is conceivable that an out of memory exception could prevent proper exception handling and error recovery, allowing the database to become corrupt. With Ghidra stopped, you may be able to identify the previous saved database state and remove the latest one. The document GhidraFilesystemStorage.html can help you navigate the storage files. If the corresponding ~NNNNNNNN.db directory has two '*.gbf" files you can remove the latest version and hope the older one is not corrupt. While a Program is open in the Code Browser Tool you can run the Ghidra script 'ConsistencyCheck' to verify the health of the program database.

[ghidra1]

Your BadDataType error I would think is unrelated, however it should not occur. The BadDataType is a special datatype that can be used in place of a deleted datatype within other datatypes such as a structure. While its constructor is private, it has a reserved ID and should be getting instantiated directly. It's unfortunate there was not a related stack trace since I will have to hunt for where the error could occur.

[axd1x8a]

I run ConsistencyCheck on the main (diff target) program and well, it took it 4 hours to say everything is okay, I haven't run it on the second one yet, but I don't think this script was made for the type of programs we are dealing with...

[ghidra1]

It inspects almost every aspect of the database. If it is huge I can see it taking a long time - although 4 hours does seem really long. Part of the issue is that memory caching will go out the window when inspecting a monster database. There are also potential failure cases which this check cannot detect (e.g., application level use of ChainedBuffers such as memory blocks). Based on your stack trace I would think it would catch that situation.

Were you able to check to see if you had an older buffer file version that may be OK?